# HG changeset patch
# User peterjc
# Date 1381480632 14400
# Node ID 44ab4c0f76839a58f27cff2ee8f425c0190b8d39
# Parent abdd608c869b046b8363b4494c02d3ae9def4a94
Uploaded v0.0.6, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence
diff -r abdd608c869b -r 44ab4c0f7683 tools/filters/seq_filter_by_id.py
--- a/tools/filters/seq_filter_by_id.py Wed Apr 24 11:34:12 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,233 +0,0 @@
-#!/usr/bin/env python
-"""Filter a FASTA, FASTQ or SSF file with IDs from a tabular file.
-
-Takes six command line options, tabular filename, ID column numbers (comma
-separated list using one based counting), input filename, input type (e.g.
-FASTA or SFF) and two output filenames (for records with and without the
-given IDs, same format as input sequence file).
-
-If either output filename is just a minus sign, that file is not created.
-This is intended to allow output for just the matched (or just the non-matched)
-records.
-
-When filtering an SFF file, any Roche XML manifest in the input file is
-preserved in both output files.
-
-Note in the default NCBI BLAST+ tabular output, the query sequence ID is
-in column one, and the ID of the match from the database is in column two.
-Here sensible values for the column numbers would therefore be "1" or "2".
-
-This tool is a short Python script which requires Biopython 1.54 or later
-for SFF file support. If you use this tool in scientific work leading to a
-publication, please cite the Biopython application note:
-
-Cock et al 2009. Biopython: freely available Python tools for computational
-molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
-
-This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute
-(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
-See accompanying text file for licence details (MIT/BSD style).
-
-This is version 0.0.5 of the script, use -v or --version to get the version.
-"""
-import sys
-
-def stop_err(msg, err=1):
- sys.stderr.write(msg.rstrip() + "\n")
- sys.exit(err)
-
-if "-v" in sys.argv or "--version" in sys.argv:
- print "v0.0.5"
- sys.exit(0)
-
-#Parse Command Line
-try:
- tabular_file, cols_arg, in_file, seq_format, out_positive_file, out_negative_file = sys.argv[1:]
-except ValueError:
- stop_err("Expected six arguments (tab file, columns, in seq, seq format, out pos, out neg), got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
-try:
- columns = [int(arg)-1 for arg in cols_arg.split(",")]
-except ValueError:
- stop_err("Expected list of columns (comma separated integers), got %s" % cols_arg)
-if min(columns) < 0:
- stop_err("Expect one-based column numbers (not zero-based counting), got %s" % cols_arg)
-
-if out_positive_file == "-" and out_negative_file == "-":
- stop_err("Neither output file requested")
-
-
-#Read tabular file and record all specified identifiers
-ids = set()
-handle = open(tabular_file, "rU")
-if len(columns)>1:
- #General case of many columns
- for line in handle:
- if line.startswith("#"):
- #Ignore comments
- continue
- parts = line.rstrip("\n").split("\t")
- for col in columns:
- ids.add(parts[col])
- print "Using %i IDs from %i columns of tabular file" % (len(ids), len(columns))
-else:
- #Single column, special case speed up
- col = columns[0]
- for line in handle:
- if not line.startswith("#"):
- ids.add(line.rstrip("\n").split("\t")[col])
- print "Using %i IDs from tabular file" % (len(ids))
-handle.close()
-
-
-def crude_fasta_iterator(handle):
- """Yields tuples, record ID and the full record as a string."""
- while True:
- line = handle.readline()
- if line == "":
- return # Premature end of file, or just empty?
- if line[0] == ">":
- break
-
- no_id_warned = False
- while True:
- if line[0] != ">":
- raise ValueError(
- "Records in Fasta files should start with '>' character")
- try:
- id = line[1:].split(None, 1)[0]
- except IndexError:
- if not no_id_warned:
- sys.stderr.write("WARNING - Malformed FASTA entry with no identifier\n")
- no_id_warned = True
- id = None
- lines = [line]
- line = handle.readline()
- while True:
- if not line:
- break
- if line[0] == ">":
- break
- lines.append(line)
- line = handle.readline()
- yield id, "".join(lines)
- if not line:
- return # StopIteration
-
-
-def fasta_filter(in_file, pos_file, neg_file, wanted):
- """FASTA filter producing 60 character line wrapped outout."""
- pos_count = neg_count = 0
- #Galaxy now requires Python 2.5+ so can use with statements,
- with open(in_file) as in_handle:
- #Doing the if statement outside the loop for speed
- #(with the downside of three very similar loops).
- if pos_file != "-" and neg_file != "-":
- print "Generating two FASTA files"
- with open(pos_file, "w") as pos_handle:
- with open(neg_file, "w") as neg_handle:
- for identifier, record in crude_fasta_iterator(in_handle):
- if identifier in wanted:
- pos_handle.write(record)
- pos_count += 1
- else:
- neg_handle.write(record)
- neg_count += 1
- elif pos_file != "-":
- print "Generating matching FASTA file"
- with open(pos_file, "w") as pos_handle:
- for identifier, record in crude_fasta_iterator(in_handle):
- if identifier in wanted:
- pos_handle.write(record)
- pos_count += 1
- else:
- neg_count += 1
- else:
- print "Generating non-matching FASTA file"
- assert neg_file != "-"
- with open(neg_file, "w") as neg_handle:
- for identifier, record in crude_fasta_iterator(in_handle):
- if identifier in wanted:
- pos_count += 1
- else:
- neg_handle.write(record)
- neg_count += 1
- return pos_count, neg_count
-
-
-if seq_format.lower()=="sff":
- #Now write filtered SFF file based on IDs from BLAST file
- try:
- from Bio.SeqIO.SffIO import SffIterator, SffWriter
- except ImportError:
- stop_err("SFF filtering requires Biopython 1.54 or later")
-
- try:
- from Bio.SeqIO.SffIO import ReadRocheXmlManifest
- except ImportError:
- #Prior to Biopython 1.56 this was a private function
- from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
- in_handle = open(in_file, "rb") #must be binary mode!
- try:
- manifest = ReadRocheXmlManifest(in_handle)
- except ValueError:
- manifest = None
- #This makes two passes though the SFF file with isn't so efficient,
- #but this makes the code simple.
- pos_count = neg_count = 0
- if out_positive_file != "-":
- out_handle = open(out_positive_file, "wb")
- writer = SffWriter(out_handle, xml=manifest)
- in_handle.seek(0) #start again after getting manifest
- pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id in ids)
- out_handle.close()
- if out_negative_file != "-":
- out_handle = open(out_negative_file, "wb")
- writer = SffWriter(out_handle, xml=manifest)
- in_handle.seek(0) #start again
- neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id not in ids)
- out_handle.close()
- #And we're done
- in_handle.close()
- #At the time of writing, Galaxy doesn't show SFF file read counts,
- #so it is useful to put them in stdout and thus shown in job info.
- print "%i with and %i without specified IDs" % (pos_count, neg_count)
-elif seq_format.lower()=="fasta":
- #Write filtered FASTA file based on IDs from tabular file
- pos_count, neg_count = fasta_filter(in_file, out_positive_file, out_negative_file, ids)
- print "%i with and %i without specified IDs" % (pos_count, neg_count)
-elif seq_format.lower().startswith("fastq"):
- #Write filtered FASTQ file based on IDs from tabular file
- from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
- reader = fastqReader(open(in_file, "rU"))
- if out_positive_file != "-" and out_negative_file != "-":
- print "Generating two FASTQ files"
- positive_writer = fastqWriter(open(out_positive_file, "w"))
- negative_writer = fastqWriter(open(out_negative_file, "w"))
- for record in reader:
- #The [1:] is because the fastaReader leaves the > on the identifier.
- if record.identifier and record.identifier.split()[0][1:] in ids:
- positive_writer.write(record)
- else:
- negative_writer.write(record)
- positive_writer.close()
- negative_writer.close()
- elif out_positive_file != "-":
- print "Generating matching FASTQ file"
- positive_writer = fastqWriter(open(out_positive_file, "w"))
- for record in reader:
- #The [1:] is because the fastaReader leaves the > on the identifier.
- if record.identifier and record.identifier.split()[0][1:] in ids:
- positive_writer.write(record)
- positive_writer.close()
- elif out_negative_file != "-":
- print "Generating non-matching FASTQ file"
- negative_writer = fastqWriter(open(out_negative_file, "w"))
- for record in reader:
- #The [1:] is because the fastaReader leaves the > on the identifier.
- if not record.identifier or record.identifier.split()[0][1:] not in ids:
- negative_writer.write(record)
- negative_writer.close()
- reader.close()
-else:
- stop_err("Unsupported file type %r" % seq_format)
diff -r abdd608c869b -r 44ab4c0f7683 tools/filters/seq_filter_by_id.txt
--- a/tools/filters/seq_filter_by_id.txt Wed Apr 24 11:34:12 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID
-=========================================================
-
-This tool is copyright 2010-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (using both the Galaxy and Biopython library
-functions) which divides a FASTA, FASTQ, or SFF file in two, those sequences with
-or without an ID present in the specified column(s) of a tabular file. Example uses
-include filtering based on search results from a tool like NCBI BLAST before
-assembly.
-
-
-Installation
-============
-
-There are just two files to install:
-
-* seq_filter_by_id.py (the Python script)
-* seq_filter_by_id.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/filters next to the tool
-for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
-tool. One suggested location is in the filters section. Simply add the line:
-
-
-
-You will also need to install Biopython 1.54 or later. That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial version, combining three separate scripts for each file format.
-v0.0.4 - Record script version when run from Galaxy.
- - Faster FASTA code which preserves the original line wrapping.
- - Basic unit test included.
-v0.0.5 - Check for errors using Python script's return code.
- - Cope with malformed FASTA entries without an identifier.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-This incorporates the previously used hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf seq_filter_by_id.tar.gz tools/filters/seq_filter_by_id.* test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
-
-Check this worked:
-
-$ tar -tzf seq_filter_by_id.tar.gz
-filter/seq_filter_by_id.py
-filter/seq_filter_by_id.txt
-filter/seq_filter_by_id.xml
-test-data/k12_ten_proteins.fasta
-test-data/k12_hypothetical.fasta
-test-data/k12_hypothetical.tabular
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
diff -r abdd608c869b -r 44ab4c0f7683 tools/filters/seq_filter_by_id.xml
--- a/tools/filters/seq_filter_by_id.xml Wed Apr 24 11:34:12 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-
- from a tabular file
- seq_filter_by_id.py --version
-
-seq_filter_by_id.py $input_tabular $columns $input_file $input_file.ext
-#if $output_choice_cond.output_choice=="both"
- $output_pos $output_neg
-#elif $output_choice_cond.output_choice=="pos"
- $output_pos -
-#elif $output_choice_cond.output_choice=="neg"
- - $output_neg
-#end if
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- output_choice_cond["output_choice"] != "neg"
-
-
-
-
-
-
-
-
-
-
-
- output_choice_cond["output_choice"] != "pos"
-
-
-
-
-
-
-
-
-
-
-
-
- Bio
-
-
-
-**What it does**
-
-By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in
-two, those sequences with or without an ID present in the tabular file column(s)
-specified. You can opt to have a single output file of just the matching records,
-or just the non-matching ones.
-
-Note that the order of sequences in the original sequence file is preserved, as
-is any Roche XML Manifest in an SFF file. Also, if any sequences share an
-identifier (which would be very unusual in SFF files), duplicates are not removed.
-
-**Example Usage**
-
-You may have performed some kind of contamination search, for example running
-BLASTN against a database of cloning vectors or bacteria, giving you a tabular
-file containing read identifiers. You could use this tool to extract only the
-reads without BLAST matches (i.e. those which do not match your contaminant
-database).
-
-You may have a file of FASTA sequences which has been used with some analysis
-tool giving tabular output, which has then been filtered on some criteria.
-You can then use this tool to divide the original FASTA file into those entries
-matching or not matching your criteria (those with or without their identifier
-in the filtered tabular file).
-
-**Citation**
-
-This tool uses Biopython to read and write SFF files. If you use this tool in
-scientific work leading to a publication, please cite the Biopython application
-note (and Galaxy too of course):
-
-Cock et al 2009. Biopython: freely available Python tools for computational
-molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
-http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
-
-
-
diff -r abdd608c869b -r 44ab4c0f7683 tools/seq_filter_by_id/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_filter_by_id/README.rst Fri Oct 11 04:37:12 2013 -0400
@@ -0,0 +1,124 @@
+Galaxy tool to filter FASTA, FASTQ or SFF sequences by ID
+=========================================================
+
+This tool is copyright 2010-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (using both the Galaxy and Biopython library
+functions) which divides a FASTA, FASTQ, or SFF file in two, those sequences with
+or without an ID present in the specified column(s) of a tabular file. Example uses
+include filtering based on search results from a tool like NCBI BLAST before
+assembly.
+
+This tool is available from the Galaxy Tool Shed at:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+
+See also sister tools:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
+
+
+Automated Installation
+======================
+
+This should be straightforward using the Galaxy Tool Shed, which should be
+able to automatically install the dependency on Biopython, and then install
+this tool and run its unit tests.
+
+
+Manual Installation
+===================
+
+There are just two files to install to use this tool from within Galaxy:
+
+* seq_filter_by_id.py (the Python script)
+* seq_filter_by_id.xml (the Galaxy tool definition)
+
+The suggested location is a dedicated tools/seq_filter_by_id folder.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. One suggested location is in the filters section. Simply add the line::
+
+
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder. Then::
+
+ $ ./run_functional_tests.sh -id seq_filter_by_id
+
+You will also need to install Biopython 1.54 or later. That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1 - Initial version, combining three separate scripts for each file format.
+v0.0.4 - Record script version when run from Galaxy.
+ - Faster FASTA code which preserves the original line wrapping.
+ - Basic unit test included.
+v0.0.5 - Check for errors using Python script's return code.
+ - Cope with malformed FASTA entries without an identifier.
+v0.0.6 - Link to Tool Shed added to help text and this documentation.
+ - Automated installation of the Biopython dependency.
+ - Use reStructuredText for this README file.
+ - Adopt standard MIT License.
+ - Updated citation information (Cock et al. 2013).
+ - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+ - Renamed folder and adopted README.rst naming.
+======= ======================================================================
+
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branches:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+ $ tar -czf seq_filter_by_id.tar.gz tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.* tools/seq_filter_by_id/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
+
+Check this worked::
+
+ $ tar -tzf seq_filter_by_id.tar.gz
+ tools/seq_filter_by_id/README.rst
+ tools/seq_filter_by_id/seq_filter_by_id.py
+ tools/seq_filter_by_id/seq_filter_by_id.xml
+ tools/seq_filter_by_id/repository_dependencies.xml
+ test-data/k12_ten_proteins.fasta
+ test-data/k12_hypothetical.fasta
+ test-data/k12_hypothetical.tabular
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r abdd608c869b -r 44ab4c0f7683 tools/seq_filter_by_id/repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_filter_by_id/repository_dependencies.xml Fri Oct 11 04:37:12 2013 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
diff -r abdd608c869b -r 44ab4c0f7683 tools/seq_filter_by_id/seq_filter_by_id.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_filter_by_id/seq_filter_by_id.py Fri Oct 11 04:37:12 2013 -0400
@@ -0,0 +1,260 @@
+#!/usr/bin/env python
+"""Filter a FASTA, FASTQ or SSF file with IDs from a tabular file.
+
+Takes six command line options, tabular filename, ID column numbers (comma
+separated list using one based counting), input filename, input type (e.g.
+FASTA or SFF) and two output filenames (for records with and without the
+given IDs, same format as input sequence file).
+
+If either output filename is just a minus sign, that file is not created.
+This is intended to allow output for just the matched (or just the non-matched)
+records.
+
+When filtering an SFF file, any Roche XML manifest in the input file is
+preserved in both output files.
+
+Note in the default NCBI BLAST+ tabular output, the query sequence ID is
+in column one, and the ID of the match from the database is in column two.
+Here sensible values for the column numbers would therefore be "1" or "2".
+
+This tool is a short Python script which requires Biopython 1.54 or later
+for SFF file support. If you use this tool in scientific work leading to a
+publication, please cite the Biopython application note:
+
+Cock et al 2009. Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+This script is copyright 2010-2013 by Peter Cock, The James Hutton Institute
+(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
+See accompanying text file for licence details (MIT license).
+
+This is version 0.1.0 of the script, use -v or --version to get the version.
+"""
+import os
+import sys
+
+def stop_err(msg, err=1):
+ sys.stderr.write(msg.rstrip() + "\n")
+ sys.exit(err)
+
+if "-v" in sys.argv or "--version" in sys.argv:
+ print "v0.1.0"
+ sys.exit(0)
+
+#Parse Command Line
+if len(sys.argv) - 1 < 7 or len(sys.argv) % 2 == 1:
+ stop_err("Expected 7 or more arguments, 5 required "
+ "(in seq, seq format, out pos, out neg, logic) "
+ "then one or more pairs (tab file, columns), "
+ "got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
+
+in_file, seq_format, out_positive_file, out_negative_file, logic = sys.argv[1:6]
+
+if not os.path.isfile(in_file):
+ stop_err("Missing input file %r" % in_file)
+if out_positive_file == "-" and out_negative_file == "-":
+ stop_err("Neither output file requested")
+if logic not in ["UNION", "INTERSECTION"]:
+ stop_err("Fifth agrument should be 'UNION' or 'INTERSECTION', not %r" % logic)
+
+identifiers = []
+for i in range((len(sys.argv) - 6) // 2):
+ tabular_file = sys.argv[6+2*i]
+ cols_arg = sys.argv[7+2*i]
+ if not os.path.isfile(tabular_file):
+ stop_err("Missing tabular identifier file %r" % tabular_file)
+ try:
+ columns = [int(arg)-1 for arg in cols_arg.split(",")]
+ except ValueError:
+ stop_err("Expected list of columns (comma separated integers), got %r" % cols_arg)
+ if min(columns) < 0:
+ stop_err("Expect one-based column numbers (not zero-based counting), got %r" % cols_arg)
+ identifiers.append((tabular_file, columns))
+
+#Read tabular file(s) and record all specified identifiers
+ids = None #Will be a set
+for tabular_file, columns in identifiers:
+ file_ids = set()
+ handle = open(tabular_file, "rU")
+ if len(columns)>1:
+ #General case of many columns
+ for line in handle:
+ if line.startswith("#"):
+ #Ignore comments
+ continue
+ parts = line.rstrip("\n").split("\t")
+ for col in columns:
+ file_ids.add(parts[col])
+ else:
+ #Single column, special case speed up
+ col = columns[0]
+ for line in handle:
+ if not line.startswith("#"):
+ file_ids.add(line.rstrip("\n").split("\t")[col])
+ print "Using %i IDs from column %s in tabular file" % (len(file_ids), ", ".join(str(col+1) for col in columns))
+ if ids is None:
+ ids = file_ids
+ if logic == "UNION":
+ ids.update(file_ids)
+ else:
+ ids.intersection_update(file_ids)
+ handle.close()
+if len(identifiers) > 1:
+ if logic == "UNION":
+ print "Have %i IDs combined from %i tabular files" % (len(ids), len(identifiers))
+ else:
+ print "Have %i IDs in common from %i tabular files" % (len(ids), len(identifiers))
+
+
+def crude_fasta_iterator(handle):
+ """Yields tuples, record ID and the full record as a string."""
+ while True:
+ line = handle.readline()
+ if line == "":
+ return # Premature end of file, or just empty?
+ if line[0] == ">":
+ break
+
+ no_id_warned = False
+ while True:
+ if line[0] != ">":
+ raise ValueError(
+ "Records in Fasta files should start with '>' character")
+ try:
+ id = line[1:].split(None, 1)[0]
+ except IndexError:
+ if not no_id_warned:
+ sys.stderr.write("WARNING - Malformed FASTA entry with no identifier\n")
+ no_id_warned = True
+ id = None
+ lines = [line]
+ line = handle.readline()
+ while True:
+ if not line:
+ break
+ if line[0] == ">":
+ break
+ lines.append(line)
+ line = handle.readline()
+ yield id, "".join(lines)
+ if not line:
+ return # StopIteration
+
+
+def fasta_filter(in_file, pos_file, neg_file, wanted):
+ """FASTA filter producing 60 character line wrapped outout."""
+ pos_count = neg_count = 0
+ #Galaxy now requires Python 2.5+ so can use with statements,
+ with open(in_file) as in_handle:
+ #Doing the if statement outside the loop for speed
+ #(with the downside of three very similar loops).
+ if pos_file != "-" and neg_file != "-":
+ print "Generating two FASTA files"
+ with open(pos_file, "w") as pos_handle:
+ with open(neg_file, "w") as neg_handle:
+ for identifier, record in crude_fasta_iterator(in_handle):
+ if identifier in wanted:
+ pos_handle.write(record)
+ pos_count += 1
+ else:
+ neg_handle.write(record)
+ neg_count += 1
+ elif pos_file != "-":
+ print "Generating matching FASTA file"
+ with open(pos_file, "w") as pos_handle:
+ for identifier, record in crude_fasta_iterator(in_handle):
+ if identifier in wanted:
+ pos_handle.write(record)
+ pos_count += 1
+ else:
+ neg_count += 1
+ else:
+ print "Generating non-matching FASTA file"
+ assert neg_file != "-"
+ with open(neg_file, "w") as neg_handle:
+ for identifier, record in crude_fasta_iterator(in_handle):
+ if identifier in wanted:
+ pos_count += 1
+ else:
+ neg_handle.write(record)
+ neg_count += 1
+ return pos_count, neg_count
+
+
+if seq_format.lower()=="sff":
+ #Now write filtered SFF file based on IDs from BLAST file
+ try:
+ from Bio.SeqIO.SffIO import SffIterator, SffWriter
+ except ImportError:
+ stop_err("SFF filtering requires Biopython 1.54 or later")
+
+ try:
+ from Bio.SeqIO.SffIO import ReadRocheXmlManifest
+ except ImportError:
+ #Prior to Biopython 1.56 this was a private function
+ from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
+ in_handle = open(in_file, "rb") #must be binary mode!
+ try:
+ manifest = ReadRocheXmlManifest(in_handle)
+ except ValueError:
+ manifest = None
+ #This makes two passes though the SFF file with isn't so efficient,
+ #but this makes the code simple.
+ pos_count = neg_count = 0
+ if out_positive_file != "-":
+ out_handle = open(out_positive_file, "wb")
+ writer = SffWriter(out_handle, xml=manifest)
+ in_handle.seek(0) #start again after getting manifest
+ pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id in ids)
+ out_handle.close()
+ if out_negative_file != "-":
+ out_handle = open(out_negative_file, "wb")
+ writer = SffWriter(out_handle, xml=manifest)
+ in_handle.seek(0) #start again
+ neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id not in ids)
+ out_handle.close()
+ #And we're done
+ in_handle.close()
+ #At the time of writing, Galaxy doesn't show SFF file read counts,
+ #so it is useful to put them in stdout and thus shown in job info.
+ print "%i with and %i without specified IDs" % (pos_count, neg_count)
+elif seq_format.lower()=="fasta":
+ #Write filtered FASTA file based on IDs from tabular file
+ pos_count, neg_count = fasta_filter(in_file, out_positive_file, out_negative_file, ids)
+ print "%i with and %i without specified IDs" % (pos_count, neg_count)
+elif seq_format.lower().startswith("fastq"):
+ #Write filtered FASTQ file based on IDs from tabular file
+ from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+ reader = fastqReader(open(in_file, "rU"))
+ if out_positive_file != "-" and out_negative_file != "-":
+ print "Generating two FASTQ files"
+ positive_writer = fastqWriter(open(out_positive_file, "w"))
+ negative_writer = fastqWriter(open(out_negative_file, "w"))
+ for record in reader:
+ #The [1:] is because the fastaReader leaves the > on the identifier.
+ if record.identifier and record.identifier.split()[0][1:] in ids:
+ positive_writer.write(record)
+ else:
+ negative_writer.write(record)
+ positive_writer.close()
+ negative_writer.close()
+ elif out_positive_file != "-":
+ print "Generating matching FASTQ file"
+ positive_writer = fastqWriter(open(out_positive_file, "w"))
+ for record in reader:
+ #The [1:] is because the fastaReader leaves the > on the identifier.
+ if record.identifier and record.identifier.split()[0][1:] in ids:
+ positive_writer.write(record)
+ positive_writer.close()
+ elif out_negative_file != "-":
+ print "Generating non-matching FASTQ file"
+ negative_writer = fastqWriter(open(out_negative_file, "w"))
+ for record in reader:
+ #The [1:] is because the fastaReader leaves the > on the identifier.
+ if not record.identifier or record.identifier.split()[0][1:] not in ids:
+ negative_writer.write(record)
+ negative_writer.close()
+ reader.close()
+else:
+ stop_err("Unsupported file type %r" % seq_format)
diff -r abdd608c869b -r 44ab4c0f7683 tools/seq_filter_by_id/seq_filter_by_id.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml Fri Oct 11 04:37:12 2013 -0400
@@ -0,0 +1,125 @@
+
+ from a tabular file
+
+ biopython
+ Bio
+
+ seq_filter_by_id.py --version
+
+seq_filter_by_id.py "$input_file" "$input_file.ext"
+#if $output_choice_cond.output_choice=="both"
+ $output_pos $output_neg
+#elif $output_choice_cond.output_choice=="pos"
+ $output_pos -
+#elif $output_choice_cond.output_choice=="neg"
+ - $output_neg
+#end if
+## TODO - Decide on best way to expose multiple ID files via the XML wrapper.
+## Single tabular file, can call the Python script with either UNION or INTERSECTION
+UNION "$input_tabular" "$columns"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ output_choice_cond["output_choice"] != "neg"
+
+
+
+
+
+
+
+
+
+
+
+ output_choice_cond["output_choice"] != "pos"
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in
+two, those sequences with or without an ID present in the tabular file column(s)
+specified. You can opt to have a single output file of just the matching records,
+or just the non-matching ones.
+
+Note that the order of sequences in the original sequence file is preserved, as
+is any Roche XML Manifest in an SFF file. Also, if any sequences share an
+identifier (which would be very unusual in SFF files), duplicates are not removed.
+
+**Example Usage**
+
+You may have performed some kind of contamination search, for example running
+BLASTN against a database of cloning vectors or bacteria, giving you a tabular
+file containing read identifiers. You could use this tool to extract only the
+reads without BLAST matches (i.e. those which do not match your contaminant
+database).
+
+You may have a file of FASTA sequences which has been used with some analysis
+tool giving tabular output, which has then been filtered on some criteria.
+You can then use this tool to divide the original FASTA file into those entries
+matching or not matching your criteria (those with or without their identifier
+in the filtered tabular file).
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This tool uses Biopython to read and write SFF files, so you may also wish to
+cite the Biopython application note (and Galaxy too of course):
+
+Cock et al (2009). Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+
+